bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of hydrolysis parameters in full‐scale anerobic digesters
Authors: Batstone D.J. , Tait S. , Starrenburg D. 
Published: October 2008

AbstractIn hydrolysis‐limited anerobic systems, the key parameters describing degradation are degradability extent (fd), and the lumped apparent first order coefficient (khyd). These are often measured in biological methane potential (BMP) tests. Using modern techniques, it should also be possible to estimate these parameters in full‐scale systems, especially where inputs are dynamic. In this study, we evaluated fd and khyd values and uncertainty based on nonlinear parameter estimation from (i) BMP tests and (ii) effluent gas and solids from two full‐scale digesters fed with highly variable feed flows and concentrations (up to 6 kg COD m−3 day−1). The substrate was thermally hydrolyzed activated sludge, and the inoculum for BMP tests was from the full‐scale digesters. While identifiability of both parameters in the BMP tests was generally good, only fd could be well identified using continuous data. For khyd using continuous data, normally only a lower limit could be found (upper was unbounded). In addition, parameters as estimated on different outputs (VS and gasflow) and two different digesters were consistent, with an fd value of 0.45–0.55, and a khyd value of >5 day−1. Gradual changes in fd over the 450 days could be related to upstream changes. fd values as estimated in BMP tests were consistent (if conservative) with continuous estimates, with a fd in BMP of 0.4–0.5. khyd values were an order of magnitude lower (0.15–0.25 day−1 vs. >5 day−1), and this translated to very poor model performance when BMP‐estimated values were used in the continuous model. This means that while BMP testing may be used for project feasibility analysis, values obtained should not be used for dynamic modeling. The parameter confidence regions found were highly nonlinear, especially for continuous systems, indicating that iterative or sampling techniques are required for an estimate of real parameter uncertainty. Biotechnol. Bioeng. 2009;102: 1513–1520. © 2008 Wiley Periodicals, Inc.
Kinetic modeling of a bi‐enzymatic system for efficient conversion of lactose to lactobionic acid
Authors: Van Hecke Wouter , Bhagwat Aditya , Ludwig Roland , Dewulf Jo , Haltrich Dietmar , Van Langenhove Herman 
Published: October 2008

AbstractA model has been developed to describe the interaction between two enzymes and an intermediary redox mediator. In this bi‐enzymatic process, the enzyme cellobiose dehydrogenase oxidizes lactose at the C‐1 position of the reducing sugar moiety to lactobionolactone, which spontaneously hydrolyzes to lactobionic acid. 2,2′‐Azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid) diammonium salt is used as electron acceptor and is continuously regenerated by laccase. Oxygen is the terminal electron acceptor and is fully reduced to water by laccase, a copper‐containing oxidase. Oxygen is added to the system by means of bubble‐free oxygenation. Using the model, the productivity of the process is investigated by simultaneous solution of the rate equations for varying enzyme quantities and redox mediator concentrations, solved with the aid of a numerical solution. The isocharts developed in this work provide an easy‐to‐use graphical tool to determine optimal process conditions. The model allows the optimization of the employed activities of the two enzymes and the redox mediator concentration for a given overall oxygen mass transfer coefficient by using the isocharts. Model predictions are well in agreement with the experimental data. Biotechnol. Bioeng. 2009;102: 1475–1482. © 2008 Wiley Periodicals, Inc.
A Novel, Q‐PCR Based Approach to Measuring Endogenous Retroviral Clearance by Capture Protein A Chromatography
Authors: Zhang Min , Lute Scott , Norling Lenore , Hong Connie , Safta Aurelia , O'Connor Deborah , Bernstein Lisa J. , Wang Hua , Blank Greg , Brorson Kurt , Chen Qi 
Published: October 2008

AbstractQuantification of virus removal by the purification process during production is required for clinical use of biopharmaceuticals. The current validation approach for virus removal by chromatography steps typically involves time‐consuming spiking experiments with expensive model viruses at bench scale. Here we propose a novel, alternative approach that can be applied in at least one instance: evaluating retroviral clearance by protein A chromatography. Our strategy uses a quantitative PCR (Q‐PCR) assay that quantifies the endogenous type C retrovirus‐like particle genomes directly in production Chinese Hamster Ovary (CHO) cell culture harvests and protein A pools. This eliminates the need to perform spiking with model viruses, and measures the real virus from the process. Using this new approach, clearance values were obtained that was comparable to those from the old model‐virus spike/removal approach. We tested the concept of design space for CHO retrovirus removal using samples from a protein A characterization study, where a wide range of chromatographic operating conditions were challenged, including load density, flow rate, wash, pooling, temperature, and resin life cycles. Little impact of these variables on CHO retrovirus clearance was found, arguing for implementation of the design space approach for viral clearance to support operational ranges and manufacturing excursions. The viral clearance results from Q‐PCR were confirmed by an orthogonal quantitative product‐enhanced reverse transcriptase (Q‐PERT) assay that quantifies CHO retrovirus by their reverse transcriptase (RT) enzyme activity. Overall, our results demonstrate that protein A chromatography is a robust retrovirus removal step and CHO retrovirus removal can be directly measured at large scale using Q‐PCR assays. Biotechnol. Bioeng. 2009;102: 1438–1447. © 2008 Wiley Periodicals, Inc.
Five year maintenance of the inducible expression of anthranilate synthase in Catharanthus roseus hairy roots
Authors: Peebles Christie A.M. , Sander Guy W. , Li Mai , Shanks Jacqueline V. , San Ka‐Yiu 
Published: October 2008

AbstractTransgenic hairy root cultures have the potential to be an industrial production platform for a variety of chemicals. This report demonstrates the long‐term stability of a transgenic Catharanthus roseus hairy root line containing the inducible expression of a feedback‐insensitive anthranilate synthase (AS). After 5 years in liquid culture, the presence of the inserted AS gene was confirmed by genomic PCR. The inducible expression of AS was confirmed by enzyme assay and by changes in terpenoid indole alkaloid concentrations. This report also demonstrates that it may take as long as 2 years for the metabolite profile to stabilize. Biotechnol. Bioeng. 2009;102: 1521–1525. © 2008 Wiley Periodicals, Inc.
Reliability of staging, prognosis, and comorbidity data collection in the National Comprehensive Cancer Network (NCCN) non‐Hodgkin lymphoma (NHL) multicenter outcomes database
Authors: Kho Michelle E. , Lepisto Eva M. , Niland Joyce C. , Friedberg Jonathan W. , LaCasce Ann S. , Weeks Jane C. 
Published: October 2008

AbstractBACKGROUND.Clinical trials and outcomes studies often rely on nonphysicians to abstract complex data from medical records, but the reliability of these data are rarely assessed.METHODS.We used standardized charts of patients with non‐Hodgkin lymphoma to assess the reliability of key clinical data elements abstracted by 6 clinical research associates (CRAs), 3 project staff, and 3 medical oncologists. We assessed reliability on 5 variables: MD‐reported and rater‐determined disease stage; International Prognostic Index (IPI; low‐low intermediate, intermediate‐high, high); Charlson comorbidity index score; and presence of any item from the Charlson index. Intraclass correlation coefficients (ICCs) of 0‐0.20 were indicative of “slight”, 0.21‐0.40 indicated “fair”, 0.41‐0.60 indicated “moderate”, 0.61‐0.80 “substantial” and >0.80 “almost perfect” reliability.RESULTS.By outcome, the ICC (95% confidence interval) values for MD‐reported stage, rater‐determined stage, and IPI were 0.86 (0.67, 0.94), 0.82 (0.59, 0.93), and 0.80 (0.55, 0.92), respectively. In contrast, the ICC (95% confidence interval) of the Charlson score, or presence of any Charlson comorbidity item was 0.47 (0.03, 0.75) and 0.61 (0.23, 0.83), respectively. Reliability varied by rater group; no rater group was consistently more reliable than others.CONCLUSIONS.Trained CRAs abstracted key clinical variables with a very high degree of reliability, and performed at a level similar to study trainers and oncologists. Elements of the Charlson index were less reliable than other data types, possibly because of inherent ambiguity in the index itself. Cancer 2008. © 2008 American Cancer Society.
Noise‐induced sampling of alternative Hamiltonian paths in quantum adiabatic search
Authors: Gaitan Frank 
Published: October 2008

AbstractWe numerically simulate the effects of noise‐induced sampling of alternative Hamiltonian paths on the ability of quantum adiabatic search (QuAdS) to solve randomly generated instances of the NP‐complete problem N‐bit Exact Cover 3. The noise‐averaged median runtime is determined as the noise‐power and number of bits N are varied, and power‐law and exponential fits are made to the data. Noise is seen to slowdown QuAdS, though a downward shift in the scaling exponent is found for N > 12 over a range of noise‐power values. We discuss whether this shift might be connected to arguments in the literature that suggest that altering the Hamiltonian path might benefit QuAdS performance. © 2008 Wiley Periodicals, Inc. Complexity, 2009
Characterization of tumor cell dissemination patterns in preclinical models of cancer metastasis using flow cytometry and laser scanning cytometry
Authors: Goodale David , Phay Carolina , Postenka Carl O. , Keeney Michael , Allan Alison L. 
Published: October 2008

AbstractThe inability to sensitively detect metastatic cells in preclinical models of cancer has created challenges for studying metastasis in experimental systems. We previously developed a flow cytometry (FCM) method for quantifying circulating tumor cells (CTCs) in mouse models of breast cancer. We have adapted this methodology for analysis of tumor dissemination to bone marrow (BM) and lymph node (LN), and for analysis of these samples by laser scanning cytometry (LSC). Our objective was to implement these methodologies for characterization of tumor cell dissemination in preclinical models of cancer metastasis. Human cancer cells were injected into mice via mammary fat pad (MFP; spontaneous metastasis), tail vein (TV; targets lung), or intracardiac (IC; targets bone) routes. At several time points postinjection (4 h to 8 weeks), mice were sacrificed and blood, LNs, and BM were collected. Samples were immunomagnetically enriched and labeled with human leukocytic antigen–fluorescein isothiocyanate and CD45‐PE antibodies (FCM/LSC), and propidium iodide (FCM) prior to quantitative analysis. Following MFP injection, CTCs increased over time, as did disseminated cells to the LN. Interestingly, tumor cells also spontaneously disseminated to BM, peaking at 2 weeks postinjection. Following TV injection, CTCs were initially high but decreased rapidly by 1 week before increasing to peak at endpoint. Combined with an observed concurrent increase in disseminated cells to LN and BM, this suggests that tumor cells may shed into the circulation from lung metastases that establish following initial cell delivery. Following IC injection, CTCs increased over time, peaking at 4 weeks. Tumor cells in the BM (most prevalent site of metastasis after IC injection) remained at moderate levels until peaking at endpoint. Combined use of FCM and LSC allows sensitive quantification of disseminated tumor cells in preclinical models of metastasis. These methods will be valuable for future studies aimed at testing new therapeutics in the metastatic setting. © 2008 International Society for Advancement of Cytometry
Ex vivo expansion of CD4+CD25+ T regulatory cells for immunosuppressive therapy
Authors: Trzonkowski Piotr , Szaryńska Magdalena , Myśliwska Jolanta , Myśliwski Andrzej 
Published: October 2008

AbstractImmunosuppressants are powerful drugs, capable of triggering severe adverse effects. Hence, there is tremendous interest in replacing them with less‐toxic agents. Adoptive therapy with CD25+CD4+ T regulatory cells (Tregs) holds promise as an alternative to immunosuppressants. Tregs have been described as the most potent immunosuppressive cells in the human body. In a number of experimental models, they have been found to quench autoimmune diseases, maintain allogeneic transplants, and prevent allergic diseases. A major stumbling block in their clinical application is related to Treg phenotype and the very limited number of these cells in the periphery, not exceeding 1–5% of total CD4+ T cells. Recent progress in multicolor flow cytometry and cell sorting as well as cellular immunology has found ways of overcoming these obstacles, and has opened the doors to the clinical application of Tregs. In the review, we describe Treg sorting and expansion techniques that have been developed in recent years. In the experience of our laboratory, as well as some published reports, Treg adoptive therapy is a promising tool in immunosuppressive therapy, and should be considered for clinical trials. © 2008 International Society for Advancement of Cytometry
Malignant first branchial cleft cysts presented as submandibular abscesses in fine‐needle aspiration: Report of three cases and review of literature
Authors: Bhanote Monisha , Yang Grace C. H. 
Published: October 2008

AbstractMalignant branchial cleft cyst is a rare entity. To the best of our knowledge, there have been one case of malignant first branchial cleft cyst and 13 cases of malignant second branchial cleft cysts in the literature that fulfill Khafif's modified criteria since 1982. We have encountered three such cases, presenting as unilateral submandibular abscesses, refractory to antibiotics, from men of 52, 53, and 61 years of age. Fine‐needle aspiration was reported as “abscess” in the first case, “atypical squamous cystic lesion” in the second case, and “atypical first branchial cleft cyst” in the third case. Histopathology showed Type II malignant first branchial cleft cysts with in situ squamous‐cell carcinoma in one patient and in situ and invasive squamous‐cell carcinoma in the other two patients. Patients are alive and disease‐free 3–4.5 years post‐surgery and ‐radiation. Awareness of this extremely rare entity can potentially avoid underdiagnosis by the cytopathologist and overtreatment by the surgeons. Diagn. Cytopathol. 2008. © 2008 Wiley‐Liss, Inc.
A retrospective study of the diagnostic accuracy of fine‐needle aspiration for breast lesions and implications for future use
Authors: Day Christina , Moatamed Neda , Fimbres Amber M. , Salami Nikki , Lim Susan , Apple Sophia K. 
Published: October 2008

AbstractIn recent years, the use of fine‐needle aspiration (FNA) in the diagnosis of breast lesions has declined in many institutions. We sought to evaluate the role of FNA for breast lesions and the annual rate of the procedure at our institution over a 4½ year period (May 2002–October 2006). A total of 831 FNAs were performed, with 258 (31%) having histologic follow‐up. The number of FNAs obtained was 159 from 5/02 to 4/03, 192 from 5/03 to 4/04, 194 from 5/04 to 4/05, 191 from 5/05 to 4/06, and 95 from 5/06 to 10/06. Each case was placed into one of four categories: nondiagnostic (9%), benign (77.5%), atypical/suspicious (5.5%), or malignant (8%). Surgical tissue was available for 37% of nondiagnostic cases, 22% of benign cases, 80% of atypical/suspicious cases, and 72% of malignant cases. The overall sensitivity and specificity for FNA was 83 and 92% respectively. The overall positive and negative predictive values were 83 and 92% respectively. There were no false‐positive cases, indicating a positive predictive value of 100% for a Dx of malignancy. For cases with surgical follow‐up, the false‐negative rate was 5.4%. Although there is a national trend away from FNAs of breast lesion, this has not been the experience at our institution. Although FNA may not be ideal in the initial evaluation of suspicious lesions, we argue that FNA for clinically benign palpable lesions and recurrent carcinomas has significant value. Diagn. Cytopathol. 2008. © 2008 Wiley‐Liss, Inc.
Cytology of metastatic appendiceal goblet cell carcinoid in pleural effusion fluid: A case report
Authors: Zafar Samiah , Chen Hua , Sun Wei , Das Kasturi 
Published: October 2008

AbstractGoblet cell appendiceal carcinoid (GCAC) is a rare neoplasm. We described the case of a 72‐year‐old man who presented with symptoms related to ascites. A computed tomography (CT) scan showed a mass involving the base of the appendix, ascites and concomitant pleural effusion. Thoracentesis of the pleural fluid showed metastatic GCAC. The appendiceal mass was biopsied and diagnosed as a GCAC. We describe the cytologic features of the metastatic GCAC to pleural fluid. To our knowledge this is the first such described case. Diagn. Cytopathol. 2008. © 2008 Wiley‐Liss, Inc.
Xenopus BTBD6 and its Drosophila homologue lute are required for neuronal development
Authors: Bury Frédéric J. , Moers Virginie , Yan Jiekun , Souopgui Jacob , Quan Xiao‐Jiang , De Geest Natalie , Kricha Sadia , Hassan Bassem A. , Bellefroid Eric J. 
Published: October 2008

AbstractBBP proteins constitute a subclass of CUL3 interacting BTB proteins whose in vivo function remains unknown. Here, we show that the Xenopus BBP gene BTBD6 and the single Drosophila homologue of mammalian BBP genes lute are strongly expressed in the developing nervous system. In Xenopus, BTBD6 expression responds positively to proneural and negatively to neurogenic gene overexpression. Knockdown of BTBD6 in Xenopus or loss of Drosophila lute result in embryos with strong defects in late neuronal markers and strongly reduced and disorganized axons while early neural development is unaffected. XBTBD6 knockdown in Xenopus also affects muscle development. Together, these data indicate that BTBD6/lute is required for proper embryogenesis and plays an essential evolutionary conserved role during neuronal development. Developmental Dynamics 237:3352–3360, 2008. © 2008 Wiley‐Liss, Inc.
Induction and modulation of smooth muscle differentiation in Xenopus embryonic cells
Authors: Barillot Wilfrid , Tréguer Karine , Faucheux Corinne , Fédou Sandrine , Thézé Nadine , Thiébaud Pierre 
Published: October 2008

AbstractBy comparison with skeletal or cardiac developmental programs, little is known regarding the specific factors that promote specification and differentiation of smooth muscle cells from pluripotent cells. We have analyzed the developmental expression of a subset of smooth muscle genes during Xenopus early development and showed that similar to mammals and avians, Xenopus smooth muscle myosin heavy chain (SM‐MHC) is a highly specific marker of smooth muscle differentiation. Embryonic cells from animal pole explants of Xenopus blastula can be induced by basic fibroblast growth factor, Wnt, and bone morphogenetic protein signals to adopt the smooth muscle pathway. Explants from early embryos that contain neural crest cells can also differentiate into cells expressing smooth muscle genes. We examined the interplay of several transcription factors, that is SRF, myocardin, and GATA6, that induce the expression of SM‐MHC in animal cap cells and found that myocardin‐dependent expression of smooth muscle genes in animal cap cells is synergized by SRF but is strongly antagonized by GATA6. Developmental Dynamics 237:3373–3386, 2008. © 2008 Wiley‐Liss, Inc.
Brain‐specific 1B promoter of FGF1 gene facilitates the isolation of neural stem/progenitor cells with self‐renewal and multipotent capacities
Authors: Hsu Yi‐Chao , Lee Don‐Ching , Chen Su‐Liang , Liao Wei‐Chih , Lin Jia‐Wei , Chiu Wen‐Ta , Chiu Ing‐Ming 
Published: October 2008

AbstractFibroblast growth factor 1 (FGF1) has been shown to maintain proliferation and self‐renewal capacities of neural stem/progenitor cells (NSPCs) in vitro. We have previously identified FGF1B as the major transcript of FGF1 gene expressed exclusively in brain areas that are known to be abundant for NSPCs in vivo. The 540‐bp (−540 to +31) sequence upstream of the 1B transcription start site (F1B) is sufficient to drive the expression of a heterologous luciferase reporter in cultured cells. In this study, we report a direct genetic and functional approach to isolate F1B(+) NSPCs using green fluorescent protein (GFP) reporter gene under the control of human F1B promoter. The F1B‐GFP reporter could facilitate the isolation of NSPCs with self‐renewal and multipotent capacities from human glioblastoma tissues, developing or adult mouse brains by fluorescence‐activated cell sorting. Future work elucidating the mechanisms that control FGF1B expression will help to identify new NSPC‐related genes. Developmental Dynamics 238:302–314, 2009. © 2008 Wiley‐Liss, Inc.
Toward understanding the development of scleral ossicles in the chicken, Gallus gallus
Authors: Franz‐Odendaal Tamara A. 
Published: October 2008

AbstractScleral ossicles are dermal bones that are present in the eye of many vertebrates. Despite this, little is understood about their development. This study investigates the cellular dynamics during and after induction, and attempts to identify inducing factors. Both cell death and proliferation were found to play limited roles in mesenchymal condensation formation, but are involved in development of the inducing epithelium overlying the presumptive ossicle. Real‐time reverse transcriptase polymerase chain reaction of candidate genes identified significant increases in sonic hedgehog (SHH) expression. In situ hybridization confirmed that SHH is exclusively expressed in the conjunctival (scleral) papillae and not in the mesenchyme. Direct localized inhibition of Hedgehog signaling, by means of cyclopamine, supports the finding that SHH may play a role in scleral ossicle induction. In addition, a nonfluctuating asymmetry with respect to the number of ossicles per eye was found. This study provides significant insight into understanding the development of the neural crest derived dermal bones. Developmental Dynamics 237:3240–3251, 2008. © 2008 Wiley‐Liss, Inc.
High‐throughput knock‐in coupling gene targeting with the HPRT minigene and Cre‐mediated recombination
Authors: Kim Tae Moon , Choi Yong Jun , Ko Jun Ho , Hasty Paul 
Published: October 2008

AbstractSingle nucleotide polymorphisms (SNPs) may influence protein function possibly contributing to phenotype; yet, for most SNPs their potential influence is unknown. Here, we present a technique in mouse embryonic stem cells that enables high‐throughput knock‐in (the placement of coding sequences adjacent to a specific endogenous promoter). Our methodology utilizes gene targeting with a combination of two selection cassettes (SAβgeo and the HPRT minigene) along with site‐specific recombinases (Cre/loxP and FLP/FRT) to efficiently introduce multiple DNA sequences, including enhanced green fluorescent protein (eGFP), adjacent to the DNA topoisomerase 3β (Top3β) promoter. This technology enables rapid and efficient introduction of DNA sequences to a specific location and advances high‐throughput analysis of many SNPs with control for expression and genetic background. genesis 46:732–737, 2008. © 2008 Wiley‐Liss, Inc.