Improving Reliability of Response Prediction to Platinum-Based Therapy by AdaBoost and Multiple Classifiers

It is a challenge to construct a reliable classifier based on microarray gene expression data for prediction of chemotherapy response, because usually only a small number of samples are available and each sample has thousands of gene expressions. This paper uses boosting and bootstrap approaches to improve the reliability of prediction. Specifically, AdaBoost and multiple classifiers based methods are used, in which support vector machines (SVMs) are utilized as the classifiers due to their good generalization ability. We compare the performance of proposed methods with a single SVM classifier system using MAS gene expression dataset in prediction of the response to platinum-based therapy for advanced-stage ovarian cancers. Statistical tests show both of the proposed methods achieve better prediction performance and have good reliability in terms of mean and standard deviation of the prediction performance for different number of selected features.

A Simple Method of Fabricating Weir-type Filters with Interdigital Aligned Full-polymer Microfluidic Channels for Blood Cell Fractionation

This paper describes a new method to fabricate large scale 3D weir-type filter for cell fractionation. The 3D structure is realized by a conformal bonding of two separate PDMS (poly-dimethyloxane) layers with in-situ microchannels which are formed by the conventional soft lithographic techniques. Moreover, the microfluidics channels on the two PDMS are set to cross to each other to increase weir numbers and flow throughput. The gap space of the weir filters depends on the thickness of the photoresist coated for the master formation, thereby it can be defined as required from submicron to hundreds micron scale. A white blood cells (WBCs) extraction experiments with the full polymer fabricated filters are conducted to validate the proposed method.. The experimental results show that the weir-type filter array can fractionate the WBCs well from blood samples. Due to its intrinsic advantages of rapid process, high throughput and low cost, the proposed method is very promising for being integrated into Micro Total analysis System (μTAS).

Arsenic trioxide and acute promyelocytic leukemia: clinical and biological

Arsenic has recently been identified as an effective drug in the treatment of newly diagnosed and relapsed acute promyelocytic leukemia. Indeed, arsenic trioxide combined with all-trans retinoic acid shows a synergistic effect. Mechanistically, arsenic targets the key leukemogenic protein PML-RARalpha, setting up a new example of molecular target-based cancer therapy.

Visualizing early frog development with motion-sensitive 3-D optical coherence microscopy

A motion-sensitive en-face-scanning 3-D optical coherence microscope (OCM) has been designed and constructed to study critical events in the early development of plants and animals. We describe the OCM instrument and present time-lapse movies of frog gastrulation, an early developmental event in which three distinct tissue layers are established that later give rise to all major organ systems. OCM images constructed with fringe-amplitude data show the mesendoderm migrating up along the blastocoel roof, thus forming the inner two tissue layers. Motion-sigma data, measuring the random motion of scatterers, is used to construct complementary images that indicate the presence of Brownian motion in the yolk cells of the endoderm. This random motion provides additional intrinsic contrast that helps to distinguish different tissue types. Depth penetration at 850 nm is sufficient for studies of the outer ectoderm layer, but is not quite adequate for detailed study of the blastocoel floor, about 500 to 800 mum deep into the embryo. However, we measure the optical attenuation of these embryos to be about 35% less at 1310 nm. 2-D OCT images at 1310 nm are presented that promise sufficient depth penetration to test current models of cell movement near the blastocoel floor during gastrulation.

Enhanced T-cell immunity induced by dendritic cells with phagocytosis of heat shock protein 70 gene-transfected tumor cells in early phase of apoptosis

The dual role of heat shock protein 70 (HSP70), as antigenic peptide chaperone and danger signal, makes it especially important in dendritic cell (DC)-based vaccination. In this study, we investigated the impacts of apoptotic transgenic MCA/HSP tumor cells expressing HSP70 on DC maturation, T-cell stimulation and vaccine efficacy. We found that DCs with phagocytosis of MCA/HSP in early phase of apoptosis expressed more pMHC I complexes, stimulated stronger cytotoxic T lymphocyte (CTL) responses (40% specific killing at an E:T cell ratio of 50) and induced immune protection in 90% of mice against MCA tumor cell challenge, compared with 25% specific CTL killing activity and 60% immune protection seen in mice immunized with DC with phagocytosis of MCA/HSP in late phase of apoptosis (P<0.05). Similar results were confirmed in another EG7 tumor model also expressing HSP70. Taken together, our data demonstrate that HSP70 on apoptotic tumor cells stimulate DC maturation, and DC with phagocytosis of apoptotic tumor cells expressing HSP70 in early phase of apoptosis more efficiently induced tumor-specific CTL responses and immunity than DCs with phagocytosis of apoptotic tumor cells in late phase of apoptosis. These results may have an important impact in designing DC-based antitumor vaccines.

DNA repair capacity as a possible biomarker of breast cancer risk in female BRCA1 mutation carriers

The BRCA1 gene product helps to maintain genomic integrity through its participation in the cellular response to DNA damage: specifically, the repair of double-stranded DNA breaks. An impaired cellular response to DNA damage is a plausible mechanism whereby BRCA1 mutation carriers are at increased risk of breast cancer. Hence, an individual's capacity to repair DNA may serve as a useful biomarker of breast cancer risk. The overall aim of the current study was to identify a biomarker of DNA repair capacity that could distinguish between BRCA1 mutation carriers and non-carriers. DNA repair capacity was assessed using three validated assays: the single-cell alkaline gel electrophoresis (comet) assay, the micronucleus test, and the enumeration of gamma-H2AX nuclear foci. DNA repair capacity of peripheral blood lymphocytes from 25 cancer-free female heterozygous BRCA1 mutation carriers and 25 non-carrier controls was assessed at baseline and following cell exposure to gamma-irradiation (2 Gy). We found no significant differences in the mean tail moment, in the number of micronuclei or in the number of gamma-H2AX nuclear foci between the carriers and non-carriers at baseline, and following gamma-irradiation. These data suggest that these assays are not likely to be useful in the identification of women at a high risk for breast cancer.

Effects of RNA interference on CD80 and CD86 expression in bone marrow-derived murine dendritic cells

To investigate whether RNA interference (RNAi) induced by small interfering RNA (siRNA) could suppress CD80 and CD86 expression in bone marrow-derived murine dendritic cells (DC). The bone marrow-derived DC of mice were separated and cultured in vitro, chemically synthesized siRNA were then transferred into the cells by LipofectAMINE 2000, and the siRNA transfection efficacy was assessed by both fluorescence microscope and flow cytometry. The mRNA expression and protein synthesis were analysed by real-time RT-PCR and flow cytometry. The cell viability of transfected DC was determined by annexin V and propidium iodine staining. Transfection of bone marrow-derived murine DC with a non-silencing FITC-labelled control siRNA demonstrated a high (71.86%) transfection efficiency without affecting cellular viability. CD80-1 siRNA was the most effective siRNA to block CD80 expression in three candidates. Similarly, CD86-3 siRNA was extraordinarily effective in repressing the expression of CD86. Cotransfection of siRNA specific to CD80 and CD86 can enhance gene silencing that is not affected by DC activation-inducing signals. CD80 and CD86 siRNA suppressed the expression of CD80 and CD86 to 31.05 +/- 2.41% and 25.43 +/- 0.85%, respectively, of the level in untreated cells (P < 0.05). siRNA is capable of triggering RNAi in bone marrow-derived DC; it can specifically and effectively knock down CD80 and CD86 gene expression. This approach is a useful tool by which costimulatory molecules of DC can be studied as well as a potential therapeutic option for allograft rejection.

Anomalous intracranial venous drainage associated with basal ganglia calcification

We describe the neuroradiologic findings in a 7-year-old boy with anomalous intracranial venous drainage and cerebral calcification. CT scans demonstrated that his scalp mass was a plexus of scalp veins filled through the emissary foramen, and there were cerebral calcifications. Angiography revealed bilateral sigmoid sinus atresia with most of the intracranial venous drainage via the prominent mastoid emissary veins into dilated scalp vein. The possible relationship between cerebral calcification and anomalous intracranial venous drainage is discussed.

An intrastrain variation of a 189-bp repeat region in the human cytomegalovirus replication origin

A 189-bp repeat has been reported previously to be present in the replication origin (ORI) of Human cytomegalovirus (HCMV) Towne strain and to contain essential and supporting sequences (Chen et al., Arch. Virol. 141, 13301 (1996)). In this study, clones of HCMV strain Towne were isolated and analyzed for the copy number of the 189-bp repeat within its ORI (oriLyt). Southern blot analysis revealed that out of 14 clones, two contained a dimer, two contained a tetramer, and the remaining contained a trimer of the 189-bp repeat. Nucleotide sequence analysis disclosed that, within the dimer and the tetramer, the 189-bp repeat was present in a directly repeated manner. In this way we demonstrated an HCMV intrastrain variation in the copy number of the 189-bp repeat. Dot blot hybridization and growth curve analysis showed that the clones containing the dimer or the tetramer replicated in infected cells with similar efficiencies. We conclude that the HCMV oriLyt with spatial separation of the essential flanking regions by various copy number of the 189-bp repeat acts as ORI in the viral genome.

Immunogenicity and persistence of a targeted anti-caries DNA vaccine

We have previously reported that a targeted anti-caries DNA vaccine, pGJA-P, induced accelerated and increased antibody responses compared with a non-targeted anti-caries DNA vaccine. Recently, pGJA-P/VAX, a new targeted anti-caries DNA vaccine for human trials, was constructed by replacing the pCI vector used in the construction of pGJA-P with pVAX1, the only vector authorized by the US Food and Drug Administration in clinical trials. Here, we report on our exploration of the kinetics of the antibody responses generated following pGJA-P/VAX immunization and the persistence of pGJA-P/VAX at both the inoculation site and the draining lymph nodes. Intranasal vaccination of mice with pGJA-P/VAX induced strong antibody responses that lasted for more than 6 months. Furthermore, pGJA-P/VAX could still be detected at both the inoculation site and the draining cervical lymph nodes 6 months after immunization. Thus, the persistent immune responses are likely due to the DNA depot in the host, which acts as a booster immunization.

Adenovirus-Mediated Antisense-ERK2 Gene Therapy Attenuates Chronic Allograft Nephropathy

BACKGROUND

The aim of this study was to investigate the effects of adenovirus-mediated antisense ERK2 (Adanti-ERK2) gene therapy on chronic allograft nephropathy.

METHODS

We employed a rat kidney transplantation mode (F344-->Lewis) and studied four groups: (1) controls (n = 6); (2) vector controls (n = 6); (3) an Adanti-ERK2 group (n = 10); and (4) an isograft group (n = 4). The animals were monitored for proteinuria, graft histology, infiltrating cells, and immune-related gene (interleukin-2 [IL-2] and intracellular adhesion molecule-1 [ICAM-1]) expression for 20 weeks after transplantation.

RESULTS

The control group had increasing proteinuria during the 20-week follow-up. All rats showed advanced chronic renal failure associated with strong immune cell infiltration and immune gene expression. Chronic graft injury was accelerated in the vector-control group, but no significant difference was observed compared with the control group. In contrast, the Adanti-ERK2 group showed less inflammation and improved graft histology/function compared with controls. Moreover, ERK2 protein expression in the Adanti-ERK2 group was lower than in the control group (P < .05) and vector-control group (P < .05). Furthermore, serial estimates of genes (IL-2, ICAM-1) related to chronic rejection showed significant downregulation in the Adanti-ERK2 group (P < .01).

CONCLUSIONS

Adenovirus-mediated antisense ERK2 gene therapy attenuated chronic allograft nephropathy. The protective effects of antisense ERK2 gene therapy may have derived from a blocked ERK signal transduction pathway, which reduced ERK expression as well as those of immune-related genes.

High-order-mode soliton structures in two-dimensional lattices with defocusing nonlinearity

While fundamental-mode discrete solitons have been demonstrated with both self-focusing and defocusing nonlinearity, high-order-mode localized states in waveguide lattices have been studied thus far only for the self-focusing case. In this paper, the existence and stability regimes of dipole, quadrupole, and vortex soliton structures in two-dimensional lattices induced with a defocusing nonlinearity are examined by the theoretical and numerical analysis of a generic envelope nonlinear lattice model. In particular, we find that the stability of such high-order-mode solitons is quite different from that with self-focusing nonlinearity. As a simple example, a dipole ("twisted") mode soliton with adjacent excited sites which may be stable in the focusing case becomes unstable in the defocusing regime. Our results may be relevant to other two-dimensional defocusing periodic nonlinear systems such as Bose-Einstein condensates with a positive scattering length trapped in optical lattices.

Zinc ribbon domain containing 1 protein: modulator of multidrug resistance, tumorigenesis and cell cycle

Zinc ribbon domain containing 1 (ZNRD1) gene encoding a protein consisting of two zinc ribbon domains was recently cloned from the human HLA locus. So far, ZNRD1 has been found implicated in transcription regulation and might play potential roles in mediating several biological processes, including multidrug resistance, tumorigenesis and cell cycle. This article reviewed these recent findings and provided additional information to support the role of ZNRD1 gene as a novel candidate DNA damage repair related gene.

Child passenger safety for inner-city Latinos: new approaches from the community

OBJECTIVE

Motor vehicle crashes injuries, the leading cause of death for Latino children in the United States, can be reduced by the correct use of child safety seats. This study evaluated the ability of a community health worker education program to improve proper child safety seat usage in urban low income Latino families.

METHODS

At a series of check events, proper child safety seat usage in families who had received an education intervention was compared with similar families who had not. The education intervention, provided by Latino community health workers trained as child passenger safety technicians, used videos and an office demonstrator. Members of the target community initiated the study and participated in its subsequent design and implementation.

RESULTS

The families that participated in the study were primarily Mexican with low income, education, and acculturation levels. Forty six rear facing and 44 forward facing child safety seats were checked. Families exposed to the intervention were more likely to have their child's seat within the manufacturer's recommended weight/height range, their child facing the correct direction, the harness straps positioned properly, to have not been in a crash, the harness straps snug, the harness retainer clip used correctly, the seat belt routed correctly, and the seat belt locked.

CONCLUSIONS

Exposure to an educational intervention provided by community health workers trained as child passenger safety technicians was associated with child safety seats being used more properly than seats of families not exposed to the intervention in an urban low income Latino community.

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

Glioblastoma is the most common primary malignant brain tumor of adults and one of the most lethal of all cancers. Patients with this disease have a median survival of 15 months from the time of diagnosis despite surgery, radiation, and chemotherapy. New treatment approaches are needed. Recent works suggest that glioblastoma patients may benefit from molecularly targeted therapies. Here, we address the compelling need for identification of new molecular targets. Leveraging global gene expression data from two independent sets of clinical tumor samples (n = 55 and n = 65), we identify a gene coexpression module in glioblastoma that is also present in breast cancer and significantly overlaps with the "metasignature" for undifferentiated cancer. Studies in an isogenic model system demonstrate that this module is downstream of the mutant epidermal growth factor receptor, EGFRvIII, and that it can be inhibited by the epidermal growth factor receptor tyrosine kinase inhibitor Erlotinib. We identify ASPM (abnormal spindle-like microcephaly associated) as a key gene within this module and demonstrate its overexpression in glioblastoma relative to normal brain (or body tissues). Finally, we show that ASPM inhibition by siRNA-mediated knockdown inhibits tumor cell proliferation and neural stem cell proliferation, supporting ASPM as a potential molecular target in glioblastoma. Our weighted gene coexpression network analysis provides a blueprint for leveraging genomic data to identify key control networks and molecular targets for glioblastoma, and the principle eluted from our work can be applied to other cancers.

Extreme Rank Selections for Linkage Analysis of Quantitative Trait Loci Using Selected Sib-Pairs

It is well known that linkage analysis using simple random sib-pairs has relatively low power for detecting quantitative trait loci with small genetic effects. The power can be substantially increased by using samples selected based on their trait values. Usually, samples that are obtained by truncation selection consist of random samples from a truncated trait distribution. In this article we propose an alternative method using extreme ranks for linkage analysis with selected sib-pairs. This approach approximates the truncation selection. With similar screening sizes and the same sample size of selected sib-pairs, the extreme rank selection and truncation method have similar power performance, both of which are substantially more powerful than when using random sib-pairs. Simulation results on the comparison of powers between the truncation selection and the extreme rank selection and/or random selection for linkage analysis are reported.

Preparation, characterization and epitope mapping of monoclonal antibodies specific to human mast cell carboxypeptidase

Human mast cell carboxypeptidase (hMC-CP) is a unique product of mast cells. Unlike tryptase and chymase, its potential function and expression in diseased conditions remain largely unknown. To develop an assay for hMC-CP, the recombinant fusion protein of hMC-CP and purified native skin hMC-CP was prepared, and two novel monoclonal antibodies against hMC-CP named CCP1 (IgG1 isotype) and CCP2 (IgM isotype) were raised in the present study. Epitope analysis shows that CCP1 and CCP2 antibodies recognize epitopes located in the region of amino acids 112-202 of hMC-CP, and hydrophilicity analysis implies that epitopes might be located in the amino acid residues 123-134 and 165-177. Furthermore, using a competition enzyme-linked immunosorbent assay, it was shown that the epitope recognized by CCP1 is close to that recognized by CCP2 or the two antibodies partially share the same epitope. Flow cytometry analysis shows that basophilic leukemia cell line KU812 reacts with both CCP1 and CCP2 antibodies, suggesting that this cell line expresses hMC-CP. In conclusion, although the two antibodies possess different isotypes, they may partially share the same epitope. These two antibodies will be valuable tools for the development of an assay to detect the levels of hMC-CP in the biological fluids in man.