bluuebunny/crossref_metadata_2025_split huggingface dataset:
Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA‐AFLP)
Authors: Weiberg Arne , Karlovsky Petr 
Published: July 2009

AbstractThe sources of variance and errors in transcriptomics based on the electrophoretic separation of amplified cDNA fragments were investigated using cDNA‐amplified fragment length polymorphism (AFLP). Transcriptome profiles of the plant‐pathogenic fungus Verticillium longisporum were generated by a standard cDNA‐AFLP protocol followed by electrophoretic separation of amplified DNA fragments in flatbed polyacrylamide gels with fluorescence detection as well as by capillary electrophoresis (DNA sequencer). The total variance was partitioned into contributions of cDNA synthesis, adapter ligation, preamplification, amplification, and electrophoresis. Parameters of computer‐aided peak recognition and matching were investigated and strategies improving matching success based on double passage with different signal intensity thresholds were developed. The overall quality of data was similar for cDNA‐AFLP and microarray hybridization. Variance of cDNA‐AFLP was independent of signal intensity, whereas microarray data showed higher variance for low‐intensity signals. Capillary electrophoresis significantly reduced the number of wrongly matched and unmatched signals as compared with flatbed gels. These results are also likely to apply to related electrophoresis‐based transcriptome analysis techniques such as mRNA differential display.
Optimized protocol for the 2‐DE of extracellular proteins from higher basidiomycetes inhabiting lignocellulose
Authors: Fragner Dorothea , Zomorrodi Mojtaba , Kües Ursula , Majcherczyk Andrzej 
Published: July 2009

AbstractBasidiomycetes inhabiting lignocellulose comprise an important class of filamentous fungi with ecological and biotechnological relevance. Extracellular enzymes of wood‐degrading fungi such as laccases, manganese‐dependent (or independent) peroxidases, cellulases and xylanases are of considerable interest for biotechnological applications. Still, proteomic studies of fungal secretomes based on 2‐DE can be very challenging due to low protein concentrations and variable amounts of fungal metabolites. Comparison of different standard methods for protein precipitation has demonstrated their limited applicability to fungal secretomes. The extracellular metabolites impair standard methods for protein quantification and can result in a strong overestimation of total protein. We have developed an optimized protocol for the precipitation of extracellular proteins from liquid cultures of Coprinopsis cinerea growing in an exponential phase on a complex media. We found that a considerable amount of gelatinous material can be removed from the liquid culture supernatants by high‐speed centrifugation. Fungal proteins can be effectively enriched by TCA precipitation and coprecipitated metabolites hampering 2‐DE can be removed through the application of Tris/acetone. Following our protocol makes it possible to concentrate proteins from culture supernatants and to simultaneously remove most of the impeding compounds from a given sample. We have applied this procedure in the 2‐DE of secretomes from the model organism C. cinerea as well as other basidiomycetes such as Pleurotus ostreatus, Phanerochaete chrysosporium, Polyporus brumalis and Schizophyllum commune.
Age distribution of human papillomavirus infection and cervical neoplasia reflects caveats of cervical screening policies
Authors: Chan Paul K.S. , Chang Alexander R. , Yu Mei Y. , Li Wai‐Hon , Chan May Y.M. , Yeung Apple C.M. , Cheung Tak‐Hong , Yau Tat‐Nga , Wong Sze‐Man , Yau Ching‐Wai , Ng Ho‐Keung 
Published: July 2009

AbstractAlthough a second age‐related peak of human papillomavirus (HPV) infection is observed in many populations, it does not seem to have any impact on cervical screening policies. We examined the age‐specific prevalence of HPV infection among 2,604 women enrolled for cervical screening and correlated the age at diagnosis of 2,491 cervical intraepithelial neoplasia Grade 2/3 (CIN2/3) lesions and 801 invasive cervical cancers (ICC). Two peaks of HPV infection were detected at 26–30 and 46–50 years, respectively. The first infection peak was followed by a CIN2/3 peak and an ICC peak at 5–15 and 15 years later, respectively. The second infection peak was followed by an ICC peak 20 years later, but strikingly no CIN2/3 peak was detected in between and thus eliminated an opportunity of treating the lesions at preinvasive stages. The most plausible explanation is that women at the expected second CIN2/3 peak (50–65 years) are not having Pap smears under the current opportunistic screening program. Furthermore, women of this age may have physiological retraction of the transformation zone, and CIN lesions may remain undetected if an adequate Pap smear sample is not obtained. To combat this problem, the screening program in Hong Kong needs to focus on women aged 50 years and older and a mop‐up screening up to 75 years is necessary. Bimodal peaks of HPV infection and cervical cancer are seen in many countries and the analysis of population‐specific age distribution of CIN2/3 should be an integral exercise in evaluating the effectiveness of a screening program.
Down regulation of membrane‐bound Neu3 constitutes a new potential marker for childhood acute lymphoblastic leukemia and induces apoptosis suppression of neoplastic cells
Authors: Mandal Chandan , Tringali Cristina , Mondal Susmita , Anastasia Luigi , Chandra Sarmila , Venerando Bruno , Mandal Chitra 
Published: July 2009

AbstractMembrane‐linked sialidase Neu3 is a key enzyme for the extralysosomal catabolism of gangliosides. In this respect, it regulates pivotal cell surface events, including trans‐membrane signaling, and plays an essential role in carcinogenesis. In this report, we demonstrated that acute lymphoblastic leukemia (ALL), lymphoblasts (primary cells from patients and cell lines) are characterized by a marked down‐regulation of Neu3 in terms of both gene expression (−30 to 40%) and enzymatic activity toward ganglioside GD1a (−25.6 to 30.6%), when compared with cells from healthy controls. Induced overexpression of Neu3 in the ALL‐cell line, MOLT‐4, led to a significant increase of ceramide (+66%) and to a parallel decrease of lactosylceramide (−55%). These events strongly guided lymphoblasts to apoptosis, as we assessed by the decrease in Bcl2/Bax ratio, the accumulation of Neu3 transfected cells in the sub G0–G1 phase of the cell cycle, the enhanced annexin‐V positivity, the higher cleavage of procaspase‐3. Therefore, the reduced expression of Neu3 in ALL could help lymphoblasts to survive, maintaining the cellular content of ceramide below a critical level. Interestingly, we found that Neu3 activity varied in relation to disease progression, increasing in clinical remission after chemotherapy, and decreasing again in patients that relapsed. In addition, a negative correlation was observed between Neu3 expression and the percentage of the ALL marker 9‐OAcGD3 positive cells. Consequently, Neu3 could represent a new potent biomarker in childhood ALL, to assess the efficacy of therapeutic protocols and to rapidly identify an eventual relapse.
Quantitative detection of Merkel cell virus in human tissues and possible mode of transmission
Authors: Loyo Myriam , Guerrero‐Preston Rafael , Brait Mariana , Hoque Mohmammad O. , Chuang Alice , Kim Myoung S. , Sharma Rajni , Liégeois Nanette J. , Koch Wayne M. , Califano Joseph A. , Westra William H. , Sidransky David 
Published: July 2009

AbstractMerkel Cell Virus (MCV) is a newly discovered polyomavirus, recently found in a rare skin cancer, Merkel cell carcinoma (MCC). However, MCV has also been detected in some normal tissue samples. We tested and compared the relative quantity of the MCV in a set of diverse human tissue samples with the MCC samples. The levels of MCV in MCCs were over 60 times higher than the highest values in all other tissues. Low quantities of MCV were detected in diverse tissue samples independently of malignant or benign histologic status. Higher levels of the virus were found in the upper aerodigestive tract, digestive system, and saliva compared to the lung and genitourinary system samples. These results confirm that MCV is widespread in the human body and suggest a possible fecal‐oral transmission route similar to the Hepatitis A virus. Despite widespread presence of the virus, it appears that only neuroendocrine skin cells are susceptible to transformation by MCV.
Candidate mechanisms accounting for effects of physical activity on breast carcinogenesis
Authors: Thompson Henry J. , Jiang Weiqin , Zhu Zongjian 
Published: July 2009

AbstractEvidence is strong that a reduction in risk for breast cancer is associated with moderate to vigorous physical activity (PA); however, there is limited understanding of the role of type, intensity, duration, and frequency of PA and their mechanisms in accounting for this health benefit. The objective of this review is to stimulate investigations of candidate mechanisms that may account for the effects of the intensity and duration of aerobic PA on breast cancer risk and tumor burden. Three hypotheses are considered: 1) the mTOR network hypothesis: PA inhibits carcinogenesis by suppressing the activation of the mTOR signaling network in mammary carcinomas; 2) the hormesis hypothesis: the carcinogenic response to PA is nonlinear and accounted for by a physiological cellular stress response; and 3) the metabolic reprogramming hypothesis: PA limits the amount of glucose and glutamine available to mammary carcinomas thereby inducing apoptosis because tumor‐associated metabolic programming is reversed. To link these hypotheses to systemic effects of PA, it is recommended that consideration be given to determining: 1) what contracting muscle releases into circulation or removes from circulation that would directly modulate the carcinogenic process in epithelial cells; 2) whether the effects of muscle contraction on epithelial cell carcinogenesis are exerted in an endocrine, paracrine, autocrine, or intracrine manner; and 3) if the effects of muscle contraction on malignant cells differ from effects on normal or premalignant cells that do not manifest the hallmarks of malignancy. © 2009 IUBMB IUBMB Life 61(9): 895–901, 2009
Evaluation of folate‐PAMAM for the delivery of antisense oligonucleotides to rat C6 glioma cells in vitro and in vivo
Authors: Kang Chunsheng , Yuan Xubo , Li Fei , Pu Peiyu , Yu Shizhu , Shen Changhong , Zhang Zhiyong , Zhang Yunting 
Published: July 2009

AbstractIn the current study, we evaluated the efficiency of folate‐polyamidoamine dendrimers conjugates (FA‐PAMAM) for the in situ delivery of therapeutic antisense oligonucleotides (ASODN) that could inhibit the growth of C6 glioma cells. Folic acid was coupled to the surface amino groups of G5‐PAMAM dendrimer (G5D) through a 1‐[3‐(dimethylamino)propyl]‐3‐ethylcarbodiimide bond, and ASODNs corresponding to rat epidermal growth factor receptor (EGFR) were then complexed with FA‐PAMAM. At an ASODN to PAMAM ratio of 16:1, agarose electrophoresis indicated that antisense oligonucleotides were completely complexed with PAMAM or FA‐PAMAM. The ASODN transfection rates mediated by FA‐PAMAM and PAMAM were superior to oligofectamine, resulting in greater suppression of EGFR expression and glioma cell growth. Stereotactic injection of EGFR ASODN:FA‐PAMAM complexes into established rat C6 intracranial gliomas resulted in greater suppression of tumor growth and longer survival time of tumor‐bearing rats compared with PAMAM and oligofectamine‐mediated EGFR‐ASODN therapy. The current study demonstrates the suitability of folate‐PAMAM dendrimer conjugates for efficient EGFR ASODN delivery into glioma cells, wherein they release the ASODN from the FA‐PAMAM to knock down EGFR expression in C6 glioma cells, both in vitro and in vivo. FA‐PAMAM may thus represent a novel delivery system for short oligonucleotides in glioma‐targeted therapy. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
In vivo evaluation of highly macroporous ceramic scaffolds for bone tissue engineering
Authors: Teixeira S. , Fernandes H. , Leusink A. , van Blitterswijk C. , Ferraz M. P. , Monteiro F. J. , de Boer J. 
Published: July 2009

AbstractDuring the last decades, different materials of both natural and synthetic origin have been developed with the aim of inducing and controlling osteogenic differentiation of mesenchymal stem cells (MSCs). In order for that to happen, it is necessary that the material to be implanted obey a series of requirements, namely: osteoconduction, biocompatibility, and biodegradability. Additionally, they must be low‐priced, easy to produce, shape, and store. Hydroxyapatite (HA) is a well known ceramic with a composition similar to the mineral component of bone and is highly biocompatible and easy to obtain and/or process. On the other hand, collagen is the main structural protein present in the human body and bone. In this study, a polymer replication method was applied and a highly porous HA scaffold was produced. Collagen was later incorporated to improve the biological properties of the scaffold while resembling the bone composition. The scaffolds were characterized by means of scanning electron microscopy, Fourier transform infrared spectroscopy and energy dispersive spectroscopy. In vitro and in vivo testing was performed in all scaffolds produced. The goal of this study was to evaluate the in vivo osteogenic potential of MSCs from two different species seeded on the different HA basedporous scaffolds with collagen type I. The resultsindicate that all scaffolds exhibit relevant bone formation, being more prominent in the case of the HA scaffolds. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
A time‐based potential step analysis of electrochemical impedance incorporating a constant phase element: A study of commercially pure titanium in phosphate buffered saline
Authors: Ehrensberger Mark T. , Gilbert Jeremy L. 
Published: July 2009

AbstractThe measurement of electrochemical impedance is a valuable tool to assess the electrochemical environment that exists at the surface of metallic biomaterials. This article describes the development and validation of a new technique, potential step impedance analysis (PSIA), to assess the electrochemical impedance of materials whose interface with solution can be modeled as a simplified Randles circuit that is modified with a constant phase element. PSIA is based upon applying a step change in voltage to a working electrode and analyzing the subsequent current transient response in a combined time and frequency domain technique. The solution resistance, polarization resistance, and interfacial capacitance are found directly in the time domain. The experimental current transient is numerically transformed to the frequency domain to determine the constant phase exponent, α. This combined time and frequency approach was tested using current transients generated from computer simulations, from resistor–capacitor breadboard circuits, and from commercially pure titanium samples immersed in phosphate buffered saline and polarized at −800 mV or +1000 mV versus Ag/AgCl. It was shown that PSIA calculates equivalent admittance and impedance behavior over this range of potentials when compared to standard electrochemical impedance spectroscopy. This current transient approach characterizes the frequency response of the system without the need for expensive frequency response analyzers or software. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Surface modification of silk fibroin with poly(ethylene glycol) for antiadhesion and antithrombotic applications
Authors: Vepari Charu , Matheson Douglas , Drummy Larry , Naik Rajesh , Kaplan David L. 
Published: July 2009

AbstractSilk fibroin film surfaces were PEGylated by reaction with cyanuric chloride‐activated poly(ethylene glycol) (PEG). Reactions with different concentrations of activated PEG generated films with PEG graft densities from 0.02 to 0.4 mg per square cm of silk fibroin. Increased PEGylation resulted in increased hydrophilicity as analyzed by contact angle, and a smoother morphology based on scanning electron microscopy. Increased PEGylation decreased human IgG adsorption and decreased the attachment and proliferation of human fibroblasts over two weeks. Increased concentration of PEG on the silk fibroin surfaces also decreased the proliferation of human mesenchymal stem cells and inhibited human platelet attachment. Surface PEGylated silk fibroin films could be useful antiadhesion and antithrombotic materials for biomedical applications when considered along with the unique mechanical and tailorable degradation profiles of silk fibroin. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Influence of direct laser fabrication implant topography on type IV bone: A histomorphometric study in humans
Authors: Shibli Jamil Awad , Mangano Carlo , D'avila Susana , Piattelli Adriano , Pecora Gabriele E. , Mangano Francesco , Onuma Tatiana , Cardoso Luciana A. , Ferrari Daniel Sanchez , Aguiar Kelly C. , Iezzi Giovanna 
Published: July 2009

AbstractThe aim of this histologic study was to evaluate the influence of the direct laser fabrication (DFL) surface topography on bone‐to‐implant contact (BIC%), on bone density in the threaded area (BA%) as well as bone density outside the threaded area (BD%) in type IV bone after 8 weeks of unloaded healing. Thirty patients (mean age 51.34 ± 3.06 years) received 1 micro‐implant (2.5‐mm diameter and 6‐mm length) each during conventional implant surgery in the posterior maxilla. Thirty micro‐implants with three topographies were evaluated: 10 machined (cpTi); 10 sandblasted and acid etched surface (SAE) and 10 DFL micro‐implants. After 8 weeks, the micro‐implants and the surrounding tissue were removed and prepared for histomorphometric analysis. Four micro‐implants (2 cpTi, 1 SAE and 1DLF) showed no osseointegration after the healing period. Histometric evaluation indicated that the mean BIC% was higher for the DFL and SAE surfaces (p = 0.0002). The BA% was higher for the DFL surface, although there was no difference with the SAE surface. The BD% was similar for all topographies (p > 0.05). Data suggest that the DFL and SAE surfaces presented a higher bone‐to‐implant contact rate compared with cpTi surfaces under unloaded conditions, after a healing period of 8 weeks. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Peripheral blood stem cell collection in multiple myeloma: A retrospective analysis of 6 years leukapheresis activity in 109 patients treated at the Istituto Nazionale dei Tumori of Milan
Authors: Coluccia Paola , Montefusco Vittorio , Tunesi Sara , Avella Mario , Bompadre Alvaro , Longoni Paolo , Milanesi Marco , De Carli Adriano , Ravagnani Fernando 
Published: July 2009

AbstractDouble autologous stem cell transplantation is the standard treatment in newly diagnosed multiple myeloma (MM) patients younger than 65 years; therefore, optimization of leukapheresis is crucial. We performed a retrospective analysis of 297 leukaphereses comparing semiautomated (V4.7 in 20% of collections) versus automated (V6.0 in 80%) Caridian (COBE) Spectra versions and analyzing the influence of M‐protein on the outcome. Both methods gave comparable collection efficiencies (CE%) (53.4% vs. 55.7% in V6.0 and V4.7, respectively) with similar leukapheresis time and processed volume. Harvest volume was higher in V4.7 (P < 0.0001) with similar contamination of red blood cells (RBCs) (P = 0.77) and platelets (P = 0.09) when compared with V6.0. In patients with higher peripheral white blood cells (WBCs), V6.0 with adjusted harvest volume (<700 mL), achieved similar CD34+ CE% (P = 0.39) and better enrichment of nucleated cells (P < 0.0,002) but higher RBCs (P < 0.0,001) and platelets contamination (P = 0.001), when compared with a larger cycle volume in patients with lower WBCs. In hard to mobilize patients, CD34+ CE% was significantly more efficient with V4.7 than V6.0 (P < 0.0,001). CD34+ CE% was unaffected by serologic M‐protein, but platelet CE% was higher in the absence of M‐protein (P = 0.0,003), without any reduction in peripheral patients platelets. We, therefore, conclude that in the setting of MM patients with a high WBCs count and/or low percentage of peripheral CD34+ cells, collections with V4.7 or adjusted cycle volume V6.0 gave comparable result in CD34+ CE%. RBCs and platelets contamination is higher if low cycle volume is chosen. In hard to mobilize patients, V4.7 is advisable. J. Clin. Apheresis, 2009. © 2009 Wiley‐Liss, Inc.
NAG7 promotes human nasopharyngeal carcinoma invasion through inhibition of estrogen receptor alpha and up‐regulation of JNK2/AP‐1/MMP1 pathways
Authors: Huang Chen , Wu Minghua , Tang Yunlian , Li Xiaoling , Ouyang Jue , Xiao Lan , Li Dan , Li Guiyuan 
Published: July 2009

AbstractThe NAG7, an estrogen receptor repressor, is a negative regulator of nasopharyngeal carcinoma cell growth. Here, we report that NAG7 promotes human nasopharyngeal carcinoma invasion, and we identify the mechanisms underlying this function. As a consequence of elevated NAG7 expression, the adhesion, migration, and invasive capabilities of HNE1 cells in vitro and in vivo were enhanced. NAG7 was a significant negative regulator of protein expression of estrogen receptor alpha (ERα), and activated both the JNK2/AP‐1/MMP1 and the upstream H‐Ras/p‐c‐Raf pathways. None of these effects induced by NAG7 over‐expression could be counteracted by estrogen. These observations indicate that NAG7 plays a potential role in promoting nasopharyngeal carcinoma invasion by regulation of ERα and the H‐ras/p‐c‐Raf and JNK2/AP‐1/MMP1 signaling pathways. J. Cell. Physiol. 221: 394–401, 2009. © 2009 Wiley‐Liss, Inc.
Combined T2‐weighted and diffusion‐weighted MRI for diagnosis of urinary bladder invasion in patients with prostate carcinoma
Authors: Ren Jing , Huan Yi , Li Fang , Wang He , Ge YaLi , Chang YingJuan , Yin Hong , Sun LiJun 
Published: July 2009

AbstractPurposeTo retrospectively determine the diffusion‐weighted imaging (DWI) characteristics and apparent diffusion coefficient (ADC) values of prostate carcinoma (PCa) with urinary bladder invasion, and to compare the accuracy of T2‐weighted MRI alone and T2 combined with DWI for predicting urinary bladder invasion.Materials and MethodsSixty‐eight patients with proven PCa were diagnosed with urinary bladder invasion after conventional magnetic resonance imaging (MRI) and DWI (b value = 750 sec/mm2) examinations. All the 68 cases underwent cystoscopy examination. DWI appearances of all urinary bladder invasion and a normal urinary bladder wall were analyzed, and their ADC values were measured. T2 images alone and then T2 images combined with DWI were scored for the likelihood of urinary bladder invasion on the basis of radiologists' written reports. The area under the receiver operating characteristic curve (AUC) was used to assess accuracy. Statistical significance was inferred at P < 0.05.ResultsAfter cystoscopy examination, 45 (66%) of 68 cases were pathologically proven urinary bladder invasion. The mean ADCs for urinary bladder invasion and normal urinary bladder wall were (0.963 ± 0.155) × 10−3mm2/sec and (1.517 ± 0.103) × 10−3mm2/sec, respectively. The ADC values of urinary bladder invasion were significantly lower than those of normal urinary bladder wall (P = 0.000). The AUC for T2‐weighted imaging plus DW imaging (0.861) was significantly larger than that for T2‐weighted imaging alone (0.734) or for DW imaging alone (0.703) (P < 0.001).ConclusionUrinary bladder invasion had lower ADC values compared with normal urinary bladder wall. T2 images plus DWI is significantly better than T2‐weighted imaging alone in the detection of urinary bladder invasion in patients with PCa. J. Magn. Reson. Imaging 2009. © 2009 Wiley‐Liss, Inc.